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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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PennCNV [clean_cnv.pl] WARNING: 3342 lines were skipped due to unrecognizable formats #55

Open nikmanadli opened 4 years ago

nikmanadli commented 4 years ago

Hi, I can't seem to make the clean_cnv.pl to work in PennCNV tool. The command line used is here: ./clean_cnv.pl combineseg --verbose --fraction 0.2 --signalfile ./lib/CCS_cleaned_10042020.pfb CCS_filtered.annotated3.cnv --out CCS_gapmerged.cnv

The error message is here:

NOTICE: Total of 659184 records are read from ./lib/CCS_cleaned_10042020.pfb WARNING: 3342 lines were skipped due to unrecognizable formats

The cnvfile (space-delimited) format is shown as examples below:

chr1:110228436-110232335 numsnp=23 length=3900 state=2,cn=1 sample.split1 startsnp=1:110228436_CNV_GSTM1 endsnp=1:110232335_CNV_GSTM1 chr4:69403991-69404631 numsnp=7 length=641 state=2,cn=1 sample.split1 startsnp=4:69403991_CNV_UGT2B17 endsnp=4:69404631 chr6:29782970-29783064 numsnp=14 length=95 state=2,cn=1 sample.split1 startsnp=6:29782970 endsnp=rs1077433

Please kindly help me as I have tried to combine the calls for the whole day to no avail.